The BioWare Blog has a post from BioWare co-founder Dr. Ray Muzyka confirming that criticism of the ending of Mass Effect 3 has had a massive effect on them, and they will indeed be changing the way the game ends, as they said they might. Here's a bit on their change in plans, and what lead to this point:

Building on their research, Exec Producer Casey Hudson and the team are hard at work on a number of game content initiatives that will help answer the questions, providing more clarity for those seeking further closure to their journey. You’ll hear more on this in April. We’re working hard to maintain the right balance between the artistic integrity of the original story while addressing the fan feedback we’ve received. This is in addition to our existing plan to continue providing new Mass Effect content and new full games, so rest assured that your journey in the Mass Effect universe can, and will, continue.

The reaction to the release of Mass Effect 3 has been unprecedented. On one hand, some of our loyal fans are passionately expressing their displeasure about how their game concluded; we care about this feedback, and we’re planning to directly address it. However, most folks appear to agree that the game as a whole is exceptional, with more than 75 critics giving it a perfect review score and a review average in the mid-90s. Net, I’m proud of the team, but we can and must always strive to do better.

I wonder, if you kill the queen in 1, do rachni reapers cease to be in game? Or is it just explained as 'oh, there was another rachni queen hiding somewhere'? It all feels so trite, pointless and inconsequential...

They "cloned" the queen. So if you killed the queen, you do the exact same thing, go down and fight through to see her. The only difference is if you accept her offer to help, at a point down the line, she backstabs you, pulls her workers out, and does some damage on the way.

Only real effect is a negative to your rating. Which almost certainly won't matter.

It did not go down like that for me in my game, I didn't kill the queen in ME1 though, so that's the obvious difference there.

It's still lame though, all things considered. making us choose again is just silly.